Hi,
Did you put an output filename in to create new file?
For example, fslswapdim myfile x y -z mynewfile
If you did just: fslswapdim myfile x y -z
then it will not have changed any images but just
output a matrix.
Also, note that doing x y -z will *change your left-right
orientation*! This is really dangerous as registration
will not fix this. If you think that the left-right labels
in your original image are fine then do *NOT* do
x y -z. When you ran fslswapdim it should have complained
about this left-right orientation change. If you want to swap
S-I in fslview and use fslswapdim like this then you should
also swap L-R (i.e. -x y -z if you have standard axial slices).
If you still think there's a problem in your version try:
fslswapdim $FSLDIR/data/standard/MNI152_T1_2mm_LR-masked.nii.gz -x
y -z LRTEST
and load LRTEST into fslview and see if the image is upside-down
but the labels all correct.
All the best,
Mark
On 23 Feb 2008, at 10:29, Jiří Keller, M.D. wrote:
> Hello,
> I have loaded fMRI dataset using dicomnifti package and did
> fslorient &fslswapdim. The images were upside-down. Ok, I ran
> fslswapdim x y -z to correct it and loaded file in fslview. The image
> is still upside-down, just the position markers swapped :-(. To make
> sure where the problem is I loaded nii file in SPM and tried
> coregistration and - not surprisingly - both swaped and non-swaped
> files look exactly the same. So here is my question: is it fslwapdim
> bug or am I missing something ?
>
> George
>
> P.S: On both, Ubuntu Feisty i386 nad 7.10 x64 are following packages
> have been kept back: dicomnifti fsl fslview nifti-bin so I do not
> have the most recent builds :-(
>
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